Abstract P5-02-45: An HRD scoring system based on long-focal copy number alterations predictive of PARP inhibitor response
Authors: Maria Gurileva, Nikita Kotlov, Anna Love, Alexandra Melnikova, Krystle Nomie, Nathan Fowler, Alexander Bagaev
Journal: Cancer Research (2023)

Abstract Homologous recombination deficiency (HRD) is characterized by a defective double-stranded DNA repair mechanism due to alterations in the homologous recombination (HR) pathway. Deleterious mutations in HR pathway genes can help identify potential responders to platinum-based chemotherapies and PARP inhibitors (PARPi), which promote apoptosis in HRD cells. Until recently, the use of PARPi in breast cancer (BC) was limited to advanced or metastatic disease with pathogenic or likely pathogenic germline BRCA (gBRCA) mutations. However, the use of PARPi has expanded to treat early-stage HER2-negative BC with a high risk of recurrence and gBRCA mutations, HER2-negative BC with somatic BRCA mutations, and triple-negative BC. To date, no universal method for HRD scoring is accepted; therefore, biomarkers are needed to stratify patients into PARPi responders and nonresponders more effectively. Because PARPi are used to treat HRD-driven cancers, we aimed to identify genomic consequences of HRD. For HRD-specific features, we calculated the proportion of long-focal total copy number alterations (LF-tCNA), which estimates amplification events for long-focal segments. Aneuploidy is especially prevalent in medullary, metaplastic, and invasive micropapillary BCs. These copy number variations are not necessarily consequences of HRD but can influence HRD scores. Genome-wide loss of heterozygosity (gwLOH) can be a result of HRD and used as a biomarker for HRD. We developed several scoring methods based on LF-tCNA, gwLOH, and aneuploidy scores. These scores were tested as predictors of HRD, defined as known loss-of-function germline mutations in BRCA1, BRCA2, PALB2, or BARD1 (TCGA-BRCA cohort, n = 1,032). To calculate the optimal HRD score, we used multivariate logistic regression analysis with HRD as an outcome and LF-tCNA, LOH, and ploidy as predictors. Based on the results of logistic regression, LF-tCNA and ploidy were selected to calculate HRD status. The positive and negative predictive values (PPV, NPV) were used to set the upper and lower thresholds, respectively. Samples with HRD scores above 7 (PPV) have the greatest potential for PARPi and platinum-based therapy response, while scores below -1 (NPV) were considered HRD wild type (WT). To validate the developed HRD score, we tested the score by combining BC cohorts (MSK_NCI and MET500 cohorts, n = 164) and used gBRCA1/2 pathogenic mutations as an outcome. Our HRD scoring system distinguished HRD WT from HRD-positive samples (AUC = 0.81) more effectively than a previously reported score based on LOH, telomeric-allelic imbalance (TAI), and large-scale state transitions (LST) (AUC = 0.72). We tested our HRD scoring system across tumor microenvironment molecular subtypes. The median HRD score in the basal-like subtype was increased compared to other subtypes, supporting the prevalence of gBRCA1/2 pathogenic mutations in this subtype. Moreover, the number of HRD-positive patients and the percent positive agreement, defined as the proportion of positive test results from our HRD also positive for HR mutations, were calculated for each BC subtype. Only 22% of basal-like HRD-positive samples also carried germline HR pathway mutations, which indicates 78% of HRD-positive patients who might benefit from PARPi or platinum treatment would have been missed by germline HR gene panels. This BC HRD scoring method is a promising tool for identifying HRD patients who may respond to PAPRi and platinum-based therapies, but additional studies are required for clinical validation. Citation Format: Maria Gurileva, Nikita Kotlov, Anna Love, Alexandra Melnikova, Krystle Nomie, Nathan Fowler, Alexander Bagaev. An HRD scoring system based on long-focal copy number alterations predictive of PARP inhibitor response [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-45.